Here is how it can easily be done:
You make a game, with a badass male character. You make him the most badass guy in the universe. He's buff, he's smart, he's fast, he's got mad skills. Even throw in some girls who are all over him. But have him constantly refer to his "lover" instead of his "girlfriend" or "princess." That way everybody can identify with his quest, because we'll all assume the gender of the lover is the gender we're attracted to. Then at the end of the game, once you've beaten the final boss, BLAM, you just saved a dude. It worked for Samus. Everybody thought they were a badass male bounty hunter saving the galaxy and then BLAM, you're in a bikini for no reason. And by that point, you were so attached to the character, that Nintendo got away with it, and Samus has become one of the most beloved female protagonists in gaming. I think the same could be done for a gay protagonist.
EDIT: Now I read the thread, and crap, axumblade beat me to it.
